Job ID = 6454664 SRX = SRX2458926 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:36:55 prefetch.2.10.7: 1) Downloading 'SRR5140275'... 2020-06-21T09:36:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:46 prefetch.2.10.7: 1) 'SRR5140275' was downloaded successfully Read 17876925 spots for SRR5140275/SRR5140275.sra Written 17876925 spots for SRR5140275/SRR5140275.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:35 17876925 reads; of these: 17876925 (100.00%) were unpaired; of these: 1282482 (7.17%) aligned 0 times 11580679 (64.78%) aligned exactly 1 time 5013764 (28.05%) aligned >1 times 92.83% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3306252 / 16594443 = 0.1992 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:49:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:27: 1000000 INFO @ Sun, 21 Jun 2020 18:49:32: 2000000 INFO @ Sun, 21 Jun 2020 18:49:37: 3000000 INFO @ Sun, 21 Jun 2020 18:49:43: 4000000 INFO @ Sun, 21 Jun 2020 18:49:48: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:49:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:54: 6000000 INFO @ Sun, 21 Jun 2020 18:49:57: 1000000 INFO @ Sun, 21 Jun 2020 18:50:00: 7000000 INFO @ Sun, 21 Jun 2020 18:50:03: 2000000 INFO @ Sun, 21 Jun 2020 18:50:06: 8000000 INFO @ Sun, 21 Jun 2020 18:50:09: 3000000 INFO @ Sun, 21 Jun 2020 18:50:12: 9000000 INFO @ Sun, 21 Jun 2020 18:50:15: 4000000 INFO @ Sun, 21 Jun 2020 18:50:18: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:50:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:21: 5000000 INFO @ Sun, 21 Jun 2020 18:50:25: 11000000 INFO @ Sun, 21 Jun 2020 18:50:27: 1000000 INFO @ Sun, 21 Jun 2020 18:50:28: 6000000 INFO @ Sun, 21 Jun 2020 18:50:31: 12000000 INFO @ Sun, 21 Jun 2020 18:50:33: 2000000 INFO @ Sun, 21 Jun 2020 18:50:34: 7000000 INFO @ Sun, 21 Jun 2020 18:50:37: 13000000 INFO @ Sun, 21 Jun 2020 18:50:39: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:50:39: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:50:39: #1 total tags in treatment: 13288191 INFO @ Sun, 21 Jun 2020 18:50:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:50:39: #1 tags after filtering in treatment: 13288112 INFO @ Sun, 21 Jun 2020 18:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:40: 3000000 INFO @ Sun, 21 Jun 2020 18:50:40: 8000000 INFO @ Sun, 21 Jun 2020 18:50:40: #2 number of paired peaks: 2508 INFO @ Sun, 21 Jun 2020 18:50:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:41: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 18:50:41: #2 alternative fragment length(s) may be 2,66 bps INFO @ Sun, 21 Jun 2020 18:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.05_model.r WARNING @ Sun, 21 Jun 2020 18:50:41: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:41: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Sun, 21 Jun 2020 18:50:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:50:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:46: 4000000 INFO @ Sun, 21 Jun 2020 18:50:46: 9000000 INFO @ Sun, 21 Jun 2020 18:50:52: 5000000 INFO @ Sun, 21 Jun 2020 18:50:52: 10000000 INFO @ Sun, 21 Jun 2020 18:50:58: 6000000 INFO @ Sun, 21 Jun 2020 18:50:59: 11000000 INFO @ Sun, 21 Jun 2020 18:51:04: 7000000 INFO @ Sun, 21 Jun 2020 18:51:05: 12000000 INFO @ Sun, 21 Jun 2020 18:51:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:10: 8000000 INFO @ Sun, 21 Jun 2020 18:51:11: 13000000 INFO @ Sun, 21 Jun 2020 18:51:13: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:51:13: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:51:13: #1 total tags in treatment: 13288191 INFO @ Sun, 21 Jun 2020 18:51:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:51:13: #1 tags after filtering in treatment: 13288112 INFO @ Sun, 21 Jun 2020 18:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:14: #2 number of paired peaks: 2508 INFO @ Sun, 21 Jun 2020 18:51:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:14: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 18:51:14: #2 alternative fragment length(s) may be 2,66 bps INFO @ Sun, 21 Jun 2020 18:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.10_model.r WARNING @ Sun, 21 Jun 2020 18:51:14: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:14: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Sun, 21 Jun 2020 18:51:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:51:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:16: 9000000 INFO @ Sun, 21 Jun 2020 18:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:21: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (2793 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:22: 10000000 INFO @ Sun, 21 Jun 2020 18:51:28: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:51:33: 12000000 INFO @ Sun, 21 Jun 2020 18:51:39: 13000000 INFO @ Sun, 21 Jun 2020 18:51:41: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:51:41: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:51:41: #1 total tags in treatment: 13288191 INFO @ Sun, 21 Jun 2020 18:51:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:51:41: #1 tags after filtering in treatment: 13288112 INFO @ Sun, 21 Jun 2020 18:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:42: #2 number of paired peaks: 2508 INFO @ Sun, 21 Jun 2020 18:51:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:42: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 18:51:42: #2 alternative fragment length(s) may be 2,66 bps INFO @ Sun, 21 Jun 2020 18:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.20_model.r WARNING @ Sun, 21 Jun 2020 18:51:42: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:42: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Sun, 21 Jun 2020 18:51:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:51:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:57: Done! pass1 - making usageList (535 chroms): 1 millis pass2 - checking and writing primary data (1951 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458926/SRX2458926.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:24: Done! pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (1576 records, 4 fields): 15 millis CompletedMACS2peakCalling